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fixed bug in scrub cells and updated crystfel default parameters

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Beale John Henry
2023-11-03 08:56:57 +01:00
parent 015a8817db
commit 5a2840ee3b
1 changed files with 5 additions and 5 deletions
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10
reduction_tools/crystfel_split.py
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@@ -51,7 +51,7 @@ def scrub_cells( stream ):
# example - Cell parameters 7.71784 7.78870 3.75250 nm, 90.19135 90.77553 90.19243 deg # example - Cell parameters 7.71784 7.78870 3.75250 nm, 90.19135 90.77553 90.19243 deg
# scrub clen and return - else nan # scrub clen and return - else nan
try: try:
pattern = r"Cell\sparameters\s(\d\.\d+)\s(\d\.\d+)\s(\d\.\d+)\snm,\s(\d+\.\d+)\s(\d+\.\d+)\s(\d+\.\d+)\sdeg" pattern = r"Cell\sparameters\s(\d+\.\d+)\s(\d+\.\d+)\s(\d+\.\d+)\snm,\s(\d+\.\d+)\s(\d+\.\d+)\s(\d+\.\d+)\sdeg"
cell_lst = re.findall( pattern, stream ) cell_lst = re.findall( pattern, stream )
xtals = len( cell_lst ) xtals = len( cell_lst )
if AttributeError: if AttributeError:
@@ -157,15 +157,15 @@ def write_crystfel_run( proc_dir, name, chunk, chunk_lst_file, geom_file, cell_f
run_sh.write( " --pdb={0} \\\n".format( cell_file ) ) run_sh.write( " --pdb={0} \\\n".format( cell_file ) )
run_sh.write( " --indexing=xgandalf-latt-cell \\\n" ) run_sh.write( " --indexing=xgandalf-latt-cell \\\n" )
run_sh.write( " --peaks=peakfinder8 \\\n" ) run_sh.write( " --peaks=peakfinder8 \\\n" )
run_sh.write( " --integration=rings-grad \\\n" ) run_sh.write( " --integration=rings-nograd \\\n" )
run_sh.write( " --tolerance=10.0,10.0,10.0,2,3,2 \\\n" ) run_sh.write( " --tolerance=10.0,10.0,10.0,2,3,2 \\\n" )
run_sh.write( " --threshold=10 \\\n" ) run_sh.write( " --threshold=10 \\\n" )
run_sh.write( " --min-snr=5 \\\n" ) run_sh.write( " --min-snr=5 \\\n" )
run_sh.write( " --int-radius=3,5,9 \\\n" ) run_sh.write( " --int-radius=5,7,9 \\\n" )
run_sh.write( " -j 32 \\\n" ) run_sh.write( " -j 32 \\\n" )
run_sh.write( " --no-multi \\\n" ) run_sh.write( " --multi \\\n" )
run_sh.write( " --check-peaks \\\n" ) run_sh.write( " --check-peaks \\\n" )
run_sh.write( " --no-retry \\\n" ) run_sh.write( " --retry \\\n" )
run_sh.write( " --max-res=3000 \\\n" ) run_sh.write( " --max-res=3000 \\\n" )
run_sh.write( " --min-pix-count=2 \\\n" ) run_sh.write( " --min-pix-count=2 \\\n" )
run_sh.write( " --local-bg-radius=4 \\\n" ) run_sh.write( " --local-bg-radius=4 \\\n" )